addlinearmotifs.qmd

---
title: "Add linear motifs"
author: "Cox Lab"
format: 
  html:
    toc: true
    toc-depth: 4
    toc-expand: false
    number-sections: true
    number-depth: 4
editor: source
date: today
bibliography: references.bib
---

# General

-   **Type:** - Matrix Processing
-   **Heading:** - Modifications
-   **Source code:** not public.

# Brief description

Given a column containing the sequence window centered around modification sites, linear motifs are matched to these sequences and a potential kinase or binding partner is suggested. The motifs are defined in the File `conf\motifs.txt`

Output: Same matrix with a categorical column added which contains the kinases or binding partners which are recognized based on the linear sequence motif.

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# Parameters

## Sequence window

Selected text column that contains the sequence windows around the sites (default: first text column in the matrix).

# Parameter window

![](images/modifications-add_linear_motifs-edited.png)